Draft genome of Rosenbergiella nectarea strain 8N4T provides insights into the potential role of this species in its plant host.

Background:Rosenbergiella nectarea strain 8N4T, the type species of the genus Rosenbergiella, was isolated from Amygdalus communis (almond) floral nectar. Other strains of this species were isolated from the floral nectar of Citrus paradisi (grapefruit), Nicotiana glauca (tobacco tree) and from Asphodelus aestivus. R. nectarea strain 8N4T is a Gram-negative, oxidase-negative, facultatively anaerobic bacterium in the family Enterobacteriaceae. Results:Here we describe features of this organism, together with its genome sequence and annotation. The DNA GC content is 47.38%, the assembly size is 3,294,717 bp, and the total number of genes are 3,346. The genome discloses the possible role that this species may play in the plant. The genome contains both virulence genes, like pectin lyase and hemolysin, that may harm plant cells and genes that are predicted to produce volatile compounds that may impact the visitation rates by nectar consumers, such as pollinators and nectar thieves. Conclusions:The genome of R. nectarea strain 8N4T reveals a mutualistic interaction with the plant host and a possible effect on plant pollination and fitness

The van Niel International Prize for Studies in Bacterial Systematics, awarded in 2020 to Tanja Woyke

The Senate of The University of Queensland, on the recommendation of the Executive Board of the International Committee on Systematics of Prokaryotes, is pleased to present the van Niel International Prize for Studies in Bacterial Systematics for the triennium 2017–2020 to Dr Tanja Woyke in recognition of her contributions made to the field of bacterial systemat-ics. The award, established in 1986 by Professor V. B. D. Skerman of The University of Queensland, honours the contribution of scholarship in the field of microbiology by Professor Cornelis Bernardus van Niel

Draft genome sequences of Bradyrhizobium shewense sp nov ERR11(T) and Bradyrhizobium yuanmingense CCBAU 10071(T)

The type strain of the prospective Bradyrhizobium shewense sp. nov. ERR11(T), was isolated from a nodule of the leguminous tree Erythrina brucei native to Ethiopia. The type strain Bradyrhizobium yuanmingense CCBAU 10071(T), was isolated from the nodules of Lespedeza cuneata in Beijing, China. The genomes of ERR11(T) and CCBAU 10071(T) were sequenced by DOE-JGI and deposited at the DOE-JGI genome portal as well as at the European Nucleotide Archive. The genome of ERR11(T) is 9,163,226 bp in length and has 102 scaffolds, containing 8548 protein-coding and 86 RNA genes. The CCBAU 10071(T) genome is arranged in 108 scaffolds and consists of 8,201,522 bp long and 7776 protein-coding and 85 RNA genes. Both genomes contain symbiotic genes, which are homologous to the genes found in the complete genome sequence of Bradyrhizobium diazoefficiens USDA110(T). The genes encoding for nodulation and nitrogen fixation in ERR11(T) showed high sequence similarity with homologous genes found in the draft genome of peanut-nodulating Bradyrhizobium arachidis LMG 26795(T). The nodulation genes nolYAnodD2D1YABCSUIJ-nolO-nodZ of ERR11(T) and CCBAU 10071(T) are organized in a similar way to the homologous genes identified in the genomes of USDA110(T), Bradyrhizobium ottawaense USDA 4 and Bradyrhizobium liaoningense CCBAU 05525. The genomes harbor hupSLCFHK and hypBFDE genes that code the expression of hydrogenase, an enzyme that helps rhizobia to uptake hydrogen released by the N2-fixation process and genes encoding denitrification functions napEDABC and norCBQD for nitrate and nitric oxide reduction, respectively. The genome of ERR11(T) also contains nosRZDFYLX genes encoding nitrous oxide reductase. Based on multilocus sequence analysis of housekeeping genes, the novel species, which contains eight strains formed a unique group close to the B. ottawaense branch. Genome Average Nucleotide Identity (ANI) calculated between the genome sequences of ERR11(T) and closely related sequences revealed that strains belonging to B. ottawaense branch (USDA4 and CCBAU15615), were the closest strains to the strain ERR11(T) with 95.2% ANI. Type strain ERR11(T) showed the highest DDH predicted value with CCBAU15615 (58.5%), followed by USDA 4 (53.1%). Nevertheless, the ANI and DDH values obtained between ERR11(T) and CCBAU 15615 or USDA 4 were below the cutoff values (ANI = 96.5%; DDH = 70%) for strains belonging to the same species, suggesting that ERR11(T) is a new species. Therefore, based on the phylogenetic analysis, ANI and DDH values, we formally propose the creation of B. shewense sp. nov. with strain ERR11(T) (HAMBI 3532(T)= LMG 30162(T)) as the type strain.Peer reviewe

Functional response of the soil microbial community to biochar applications

Biochar has the potential to mitigate the impacts of climate change and soil degradation by simultaneously sequestering C in soil and improving soil quality. However, the mechanism of biochar's effect on soil microbial communities remains unclear. Therefore, we conducted a global meta-analysis, where we collected 2,110 paired observations from 107 published papers and used structural equation modeling (SEM) to analyze the effects of biochar on microbial community structure and function. Our result indicated that arbuscular mycorrhizal fungal abundance, microbial biomass C, and functional richness increased with biochar addition regardless of loads, time since application, and experiment types. Results from mixed linear model analysis suggested that soil respiration and actinomycetes (ACT) abundance decreased with biochar application. With the increase of soil pH, the effect of biochar on fungal abundance and C metabolic ability was lessened. Higher biochar pH associated with higher pyrolysis temperatures reduced the abundance of bacteria, fungi, ACT, and soil microbes feeding on miscellaneous C from Biolog Eco-plate experiments. SEM that examined the effect of biochar properties, load, and soil properties on microbial community indicated that fungal abundance was the dominant factor affecting the response of the bacterial abundance to biochar. The response of bacterial abundance to biochar addition was soil dependent, whereas fungi abundance was mostly related to biochar load and pyrolysis temperature. Based on soil conditions, controlling biochar load and production conditions would be a direct way to regulate the effect of biochar application on soil microbial function and increase the capacity to sequester C

Genome sequencing suggests diverse secondary metabolism in coral-associated aquimarina megaterium

We report here the genome sequences of three Aquimarina megaterium strains isolated from the octocoral Euniceila labiata. We reveal a coding potential for versatile carbon metabolism and biosynthesis of natural products belonging to the polyketide, nonribosomal peptide, and terpene compound classes.info:eu-repo/semantics/publishedVersio

The Roseibium album (Labrenzia alba) genome possesses multiple symbiosis factors possibly underpinning host-microbe relationships in the Marine Benthos

Here, we announce the genomes of eight Roseibium album (synonym Labrenzia alba) strains that were obtained from the octocoral Eunicella labiata. Genome annotation revealed multiple symbiosis factors common to all genomes, such as eukaryotic-like repeat protein- and multidrug resistance-encoding genes, which likely underpin symbiotic relationships with marine invertebrate hosts.info:eu-repo/semantics/publishedVersio

The Diverse Bacterial Community in Intertidal, Anaerobic Sediments at Sapelo Island, Georgia

The phylogenetic diversity and composition of the bacterial community in anaerobic sediments from Sapelo Island, GA, USA were examined using 16S rRNA gene libraries. The diversity of this community was comparable to that of soil, and 1,186 clones formed 817 OTUs at 99% sequence similarity. Chao1 estimators for the total richness were also high, at 3,290 OTUs at 99% sequence similarity. The program RDPquery was developed to assign clones to taxonomic groups based upon comparisons to the RDP database. While most clones could be assigned to describe phyla, fewer than 30% of the clones could be assigned to a described order. Similarly, nearly 25% of the clones were only distantly related (<90% sequence similarity) to other environmental clones, illustrating the unique composition of this community. One quarter of the clones were related to one or more undescribed orders within the γ-Proteobacteria. Other abundant groups included the δ-Proteobacteria, Bacteroidetes, and Cyanobacteria. While these phyla were abundant in other estuarine sediments, the specific members at Sapelo Island appeared to be different from those previously described in other locations, suggesting that great diversity exists between as well as within estuarine intertidal sediments. In spite of the large differences in pore water chemistry with season and depth, differences in the bacterial community were modest over the temporal and spatial scales examined and generally restricted to only certain taxa

The Nbp35/ApbC homolog acts as a nonessential [4Fe-4S] transfer protein in methanogenic archaea

© 2019 Federation of European Biochemical Societies The nucleotide binding protein 35 (Nbp35)/cytosolic Fe-S cluster deficient 1 (Cfd1)/alternative pyrimidine biosynthetic protein C (ApbC) protein homologs have been identified in all three domains of life. In eukaryotes, the Nbp35/Cfd1 heterocomplex is an essential Fe-S cluster assembly scaffold required for the maturation of Fe-S proteins in the cytosol and nucleus, whereas the bacterial ApbC is an Fe-S cluster transfer protein only involved in the maturation of a specific target protein. Here, we show that the Nbp35/ApbC homolog MMP0704 purified from its native archaeal host Methanococcus maripaludis contains a [4Fe-4S] cluster that can be transferred to a [4Fe-4S] apoprotein. Deletion of mmp0704 from M. maripaludis does not cause growth deficiency under our tested conditions. Our data indicate that Nbp35/ApbC is a nonessential [4Fe-4S] cluster transfer protein in methanogenic archaea

Speech Communication

Contains research objectives and three research projects.U. S. Air Force (Electronic Systems Division) under Contract AF 19(604)-6102National Science Foundation (Grant G-16526)National Institutes of Health (Grant MH-04737-02

Hymenobacter artigasi sp. nov., isolated from air sampling in maritime Antarctica

A rod-shaped and Gram-stain-negative bacterial strain, 1BT, was isolated from an air sample collected at King George Island, maritime Antarctica. Strain 1BT is strictly aerobic, psychrophilic, catalase-positive, oxidase-positive and non-motile. Growth of strain 1BT is observed at 0–20 °C (optimum, 10 °C), pH 6.0–8.0 (optimum, pH 8.0) and in the presence of 0–1.0% NaCl (optimum, 0.5 % NaCl). Phylogenetic analysis based on 16S rRNA gene sequences places strain 1BT within the genus Hymenobacter and shows the highest similarity to Hymenobacter antarcticus VUG-A42aaT (97.5 %). The predominant menaquinone of strain 1BT is MK-7 and the major fatty acids (>10 %) comprise summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c; 32.5 %), iso-C15 : 0 (17.6 %) and anteiso C15 : 0 (12.3 %). The polar lipid profile consists of the major compounds phosphatidylethanolamine, phosphatidylserine, two unidentified aminolipids and one unidentified phospholipid. The DNA G+C content based on the draft genome sequence is 61.2 mol%. Based on the data from the current polyphasic study, 1BT represents a novel species of the genus Hymenobacter , for which the name Hymenobacter artigasi sp. nov. is suggested. The type strain is 1BT (=CCM 8970T=CGMCC 1.16843T)